Description Usage Arguments Details Value References See Also Examples
A function that infers the interaction network using the CLR algorithm.
1 | clr(mi)
|
mi |
matrix of the mutual information. |
CLR computes the score
sqrt(zi^2 + zj^2)
for each pair of variables i, j, where
zi = max(0, ( I(Xi;Xj)-mean(Xi) ) / sd(Xi))
and mean(Xi) and sd(Xi) are the mean and the standard deviation of the mutual information values I(Xi;Xk) for all k=1,…,n.
By default, the function uses all the available cores. You can
set the actual number of threads used to N by exporting the
environment variable OMP_NUM_THREADS=N
.
A square weighted adjacency matrix of the inferred network.
Jeremiah J. Faith, Boris Hayete, Joshua T. Thaden, Ilaria Mogno, Jamey Wierzbowski, Guillaume Cottarel, Simon Kasif, James J. Collins, and Timothy S. Gardner. Large-scale mapping and validation of escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biology, 2007.
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